Li Xianfeng, Latour Robert A
Department of Bioengineering, Clemson University, Clemson, South Carolina 29634.
Polymer (Guildf). 2009 Jul 31;50(16):4139-4149. doi: 10.1016/j.polymer.2009.06.055.
A systematic procedure has been developed to construct a relaxed dense-phase atomistic structure of a complex amorphous polymer. The numerical procedure consists of (1) coarse graining the atomistic model of the polymer into a mesoscopic model based on an iterative algorithm for potential inversion from distribution functions of the atomistic model, (2) relaxation of the coarse grained chain using a molecular dynamics scheme, and (3) recovery of the atomistic structure by reverse mapping based on the superposition of atomistic counterparts on the corresponding coarse grained coordinates. These methods are demonstrated by their application to construct a relaxed, dense-phase model of poly(DTB succinate), which is an amorphous tyrosine-derived biodegradable polymer that is being developed for biomedical applications. Both static and dynamic properties from the coarse-grained and atomistic simulations are analyzed and compared. The coarse-grained model, which contains the essential features of the DTB succinate structure, successfully described both local and global structural properties of the atomistic chain. The effective speedup compared to the corresponding atomistic simulation is substantially above 10(2), thus enabling simulation times to reach well into the characteristic experimental regime. The computational approach for reversibly bridging between coarse-grained and atomistic models provides an efficient method to produce relaxed dense-phase all-atom molecular models of complex amorphous polymers that can subsequently be used to study and predict the atomistic-level behavior of the polymer under different environmental conditions in order to optimally design polymers for targeted applications.
已开发出一种系统程序，用于构建复杂非晶态聚合物的松弛密相原子结构。该数值程序包括：(1)基于原子模型分布函数的势反转迭代算法，将聚合物的原子模型粗粒化为介观模型；(2)使用分子动力学方案对粗粒化链进行松弛；(3)基于原子对应物在相应粗粒化坐标上的叠加，通过反向映射恢复原子结构。通过将这些方法应用于构建聚（DTB琥珀酸酯）的松弛密相模型来进行演示，聚（DTB琥珀酸酯）是一种非晶态酪氨酸衍生的可生物降解聚合物，正被开发用于生物医学应用。分析并比较了粗粒化模拟和原子模拟的静态和动态特性。包含DTB琥珀酸酯结构基本特征的粗粒化模型成功地描述了原子链的局部和全局结构特性。与相应的原子模拟相比，有效加速比大大超过10(2)，从而使模拟时间能够很好地达到特征实验范围。在粗粒化模型和原子模型之间进行可逆桥接的计算方法提供了一种有效的方法，来生成复杂非晶态聚合物的松弛密相全原子分子模型，随后可用于研究和预测聚合物在不同环境条件下的原子级行为，以便为目标应用优化设计聚合物。
